diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/search.py | 77 |
1 files changed, 64 insertions, 13 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py index aa844ee..755f975 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -21,7 +21,8 @@ search = Blueprint("search", __name__) ChromosomalPosition = namedtuple("ChromosomalPosition", "chromosome position") ChromosomalInterval = namedtuple("ChromosomalInterval", "chromosome start end") -IntervalLiftoverFunction = Callable[[ChromosomalInterval], Maybe[ChromosomalInterval]] +IntervalLiftoverFunction = Callable[[ + ChromosomalInterval], Maybe[ChromosomalInterval]] FieldProcessorFunction = Callable[[str], xapian.Query] @@ -50,9 +51,11 @@ class FieldProcessor(xapian.FieldProcessor): additional state required by the field processor is contained in the lexical environment of the closure. """ + def __init__(self, proc: FieldProcessorFunction) -> None: super().__init__() self.proc = proc + def __call__(self, query: str) -> xapian.Query: return self.proc(query) @@ -83,7 +86,7 @@ def liftover(chain_file: Path, position: ChromosomalPosition) -> Maybe[Chromosom if line.startswith('chain'): (target, query, query_size, query_strand) = split_chain_line(line) if (target.chromosome == position.chromosome - and target.start <= position.position < target.end): + and target.start <= position.position < target.end): transformed_position = query.start + position.position - target.start if query_strand == '-': transformed_position = query_size - 1 - transformed_position @@ -113,8 +116,9 @@ def liftover_interval(chain_file: str, interval: ChromosomalInterval) -> Chromos # practice. But, in this case, there doesn't seem to be a way # around. .map(lambda interval: ChromosomalInterval(interval.chromosome, - Just(min(interval.start.value, interval.end.value)), - Just(max(interval.start.value, interval.end.value))) + Just( + min(interval.start.value, interval.end.value)), + Just(max(interval.start.value, interval.end.value))) if interval.start.is_just() and interval.end.is_just() else interval)) @@ -139,7 +143,7 @@ def parse_position(spec: str) -> tuple[Maybe[int], Maybe[int]]: """Parse position specifiation converting point locations to ranges.""" # Range if ".." in spec: - return tuple(limit.map(apply_si_suffix) # type: ignore + return tuple(limit.map(apply_si_suffix) # type: ignore for limit in parse_range(spec)) # If point location, assume +/- 50 kbases on either side. else: @@ -152,9 +156,9 @@ def parse_position_field(location_slot: int, query: bytes) -> xapian.Query: """Parse position and return a xapian query.""" start, end = parse_position(query.decode("utf-8")) # TODO: Convert the xapian index to use bases instead of megabases. - to_megabases = lambda x: str(Decimal(x)/10**6) + def to_megabases(x): return str(Decimal(x)/10**6) return (xapian.NumberRangeProcessor(location_slot) - (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore + (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore def parse_location_field(species_query: xapian.Query, @@ -176,10 +180,11 @@ def parse_location_field(species_query: xapian.Query, def make_query(interval: ChromosomalInterval) -> xapian.Query: # TODO: Convert the xapian index to use bases instead of megabases. - to_megabases = lambda x: str(Decimal(x)/10**6) + def to_megabases(x): return str(Decimal(x)/10**6) return combine_queries(xapian.Query.OP_AND, species_query, - xapian.Query(chromosome_prefix + interval.chromosome), + xapian.Query(chromosome_prefix + + interval.chromosome), xapian.NumberRangeProcessor(location_slot) (interval.start.maybe("", to_megabases), interval.end.maybe("", to_megabases))) @@ -213,12 +218,14 @@ def parse_query(synteny_files_directory: Path, query: str): for i, prefix in enumerate(range_prefixes): # Treat position specially since it needs its own field processor. if prefix == "position": - position_field_processor = FieldProcessor(partial(parse_position_field, i)) + position_field_processor = FieldProcessor( + partial(parse_position_field, i)) queryparser.add_boolean_prefix(prefix, position_field_processor) # Alias the position prefix with pos. queryparser.add_boolean_prefix("pos", position_field_processor) else: - queryparser.add_rangeprocessor(xapian.NumberRangeProcessor(i, prefix + ":")) + queryparser.add_rangeprocessor( + xapian.NumberRangeProcessor(i, prefix + ":")) # Add field processors for synteny triplets. species_shorthands = {"Hs": "human", @@ -265,10 +272,13 @@ def search_results(): if results_per_page > maximum_results_per_page: abort(400, description="Requested too many search results") - query = parse_query(Path(current_app.config["DATA_DIR"]) / "synteny", querystring) + query = parse_query( + Path(current_app.config["DATA_DIR"]) / "synteny", querystring) traits = [] # pylint: disable=invalid-name - with xapian_database(current_app.config["XAPIAN_DB_PATH"]) as db: + + xapian_db_path = "/tmp/xapian" + with xapian_database(xapian_db_path) as db: enquire = xapian.Enquire(db) # Filter documents by type. enquire.set_query(xapian.Query(xapian.Query.OP_FILTER, @@ -286,3 +296,44 @@ def search_results(): "dopt": "Abstract"})) traits.append(trait.data) return jsonify(traits) + + +NGRAM_MIN_LENGTH = 2 +NGRAM_MAX_LENGTH = 15 + + +def edge_ngram_terms(values, min_len=NGRAM_MIN_LENGTH, max_len=NGRAM_MAX_LENGTH): + prefixes = [] + + values = values.split() + for word in values: + for i in range(max(len(word), min_len), min(len(word), max_len) + 1): + prefix = word[:i] + prefixes.append(prefix) + return prefixes + + +@search.route("/autocomplete") +def autocomplete(): + #!expirementall + querystring = request.args.get("query", default="") + # modify xapian path + with xapian_database("/tmp/xapian") as db: + queryparser = xapian.QueryParser() + queryparser.set_stemmer(xapian.Stem('en')) + queryparser.set_stemming_strategy(queryparser.STEM_NONE) + # trial and prefixes for other parse the query + queryparser.add_prefix("species", "XS") + queries = queryparser.parse_query(querystring) + init_term = queries._get_terms_begin() + filtered = set() + while init_term != queries._get_terms_end(): + filtered.add(init_term.get_term().decode()) + next(init_term) + matched = set() + for val in edge_ngram_terms(" ".join(filtered)): + matched.update({val.decode() + for val in [term.term for term in db.allterms(val)]}) + return jsonify({ + "autocomplete": sorted(matched, key=len) + }) |